Measure herbarium representativeness

This guide demonstrates how to use the jabot_coverage() function in the jabotR package to measure how well a JABOT-hosted herbarium represents the species diversity recognized by the Flora e Funga do Brasil (FFB).

Function Overview

Unlike jabot_gaps(), which focuses on species that are missing from a collection, jabot_coverage() characterizes the species that are represented. Overall coverage is the number of FFB species held by the herbarium divided by the total number of FFB species, multiplied by 100.

The analysis includes overall FFB species coverage, coverage by taxonomic group/family/phytogeographic domain/Brazilian state, coverage of endemic versus non-endemic species, representation of type material, graphical summaries, and a self-contained HTML report.

This tool is ideal for reporting collection strengths — e.g. for institutional assessments, grant applications, or deciding which taxonomic groups a herbarium already represents well.

Arguments

Argument	Description
herbarium	Herbarium acronym in uppercase (e.g. "RB").
jabot_path	Path to a directory with previously downloaded JABOT DwC-A files. NULL downloads automatically.
format	Static formats to save individual figures: "pdf", "png", or both. The HTML report is always generated regardless.
fig_width, fig_height	Dimensions (in inches) of saved figures.
open_report	If TRUE, opens the HTML report in the default browser after rendering.
verbose	If TRUE, prints progress messages.
dir	Output directory. Defaults to "<herbarium>_representativeness".

Basic Use Case

coverage_analysis <- jabot_coverage(herbarium = "RB",
                                    verbose = TRUE,
                                    open_report = TRUE,
                                    dir = "RB_representativeness")

Exporting Individual Figures

coverage_analysis <- jabot_coverage(herbarium = "RB",
                                    format = c("pdf", "png"),
                                    verbose = TRUE,
                                    open_report = TRUE,
                                    dir = "RB_representativeness")

Reusing a Previously Downloaded Dataset

coverage_analysis <- jabot_coverage(herbarium = "RB",
                                    jabot_path = "jabot_download",
                                    format = "pdf",
                                    verbose = TRUE,
                                    open_report = TRUE,
                                    dir = "RB_representativeness")

Example Output

The HTML report ranks families by how well they are covered, and maps overall coverage percentage by Brazilian state:

Best- and worst-covered families in the jabot_coverage() HTML report

Choropleth map of herbarium coverage by Brazilian state

The function also returns (invisibly) a named list with every computed data frame, so summary numbers can be pulled directly into other analyses:

coverage_analysis$coverage_pct
coverage_analysis$endemic_coverage_pct
head(coverage_analysis$family_rep)

Tips

• Coverage and gaps are two views of the same comparison — run jabot_coverage() alongside jabot_gaps() for a complete picture of a herbarium’s standing against FFB.
• endemic_coverage_pct is often lower than overall coverage; it highlights Brazilian endemics that are especially valuable to prioritize for future collecting.
• Supply jabot_path on repeated runs to avoid re-downloading FFB and JABOT data.

See Also

• Identify taxonomic gaps: jabot_gaps()
• Locate missing species and collecting priorities: jabot_missing()
• jabot_records(): Retrieve taxon-specific specimens